Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001800.1 Hibiscus syriacus cultivar Beakdansim tig00003639_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88674
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:3532 original size:21 final size:21
Alignment explanation
Indices: 3506--3545 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3496 CAGAACCCCA
*
3506 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3527 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3546 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3554 original size:23 final size:21
Alignment explanation
Indices: 3528--3586 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3518 TTCCCCTGTG
3528 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
3551 GGGGGAAGCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
* *
3571 GGGGGGATCGATTCCC
1 GGGGGAATCGGTTCCC
3587 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:3575 original size:21 final size:23
Alignment explanation
Indices: 3527--3577 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3517 ATTCCCCTGT
*
3527 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAAGCGGTTCCCCTTCAA
*
3550 AGGGGGAAGCGGTT-CCC-TCAA
1 GGGGGGAAGCGGTTCCCCTTCAA
3571 GGGGGGA
1 GGGGGGA
3578 TCGATTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.16
Consensus pattern (23 bp):
GGGGGGAAGCGGTTCCCCTTCAA
Found at i:14212 original size:18 final size:18
Alignment explanation
Indices: 14191--14230 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
14181 GTTTGAATAA
14191 ATATTAT-TCTATATAATT
1 ATATTATAT-TATATAATT
*
14209 ATATTATATTATATTATT
1 ATATTATATTATATAATT
14227 ATAT
1 ATAT
14231 CAACAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTATATAATT
Found at i:14565 original size:60 final size:60
Alignment explanation
Indices: 14472--14649 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 60
14462 TCCCTCAACC
* * **
14472 ATGACTCTCGTTAC-AAATTAGT-CTTGAAACTTTTAAATACTCCAATTTCATCCTTAAACT
1 ATGACTCTCATT-CTAAATTAGTCCTT-AAACTTTTAAATACTTCAATTTCATCCCCAAACT
* * * *
14532 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTAAATTTCATCCCCAAACT
1 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATACTTCAATTTCATCCCCAAACT
* * * * *
14592 ATGAATCTCATTCTAAATTGGTCCCTCAACTTTTAGAT-CTTTCAATTTCATCCCCAAA
1 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATAC-TTCAATTTCATCCCCAAA
14650 TTCATTCAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 94 0.96
61 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATACTTCAATTTCATCCCCAAACT
Found at i:17113 original size:23 final size:23
Alignment explanation
Indices: 17087--17136 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17077 ATAATATAAC
* *
17087 ACACACACATATATATATATGCA
1 ACACACACACACATATATATGCA
**
17110 ACACGTACACACATATATATGCA
1 ACACACACACACATATATATGCA
17133 ACAC
1 ACAC
17137 GTGCAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (23 bp):
ACACACACACACATATATATGCA
Found at i:17177 original size:19 final size:21
Alignment explanation
Indices: 17153--17191 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17143 CTATAATAAT
*
17153 CAATTA-A-ATAAACATGTAG
1 CAATTATATATAAAAATGTAG
17172 CAATTATATATAAAAATGTA
1 CAATTATATATAAAAATGTA
17192 CAAATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
CAATTATATATAAAAATGTAG
Found at i:23390 original size:20 final size:20
Alignment explanation
Indices: 23365--23405 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23355 CAAAAAGCCT
23365 ACTGGAATATTGGTATCGAG
1 ACTGGAATATTGGTATCGAG
* *
23385 ACTGGAATGTTGGTTTCGAG
1 ACTGGAATATTGGTATCGAG
23405 A
1 A
23406 TTGACATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (20 bp):
ACTGGAATATTGGTATCGAG
Found at i:25727 original size:19 final size:19
Alignment explanation
Indices: 25703--25739 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25693 ATGACCAACA
*
25703 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
25722 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
25740 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:25848 original size:20 final size:20
Alignment explanation
Indices: 25825--25958 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
25815 GAATATGTAA
25825 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
25845 ATCGCAACGTAATTCTGACT
1 ATCGCAACGCGATTCTGACT
** *
25865 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATTCTGAC--T
*
25886 ATTGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
25906 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
25926 ATCGCAACGTGATCCTGACT
1 ATCGCAACGCGATTCTGACT
*
25946 ATCACAACGCGAT
1 ATCGCAACGCGAT
25959 AATAAAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 76 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:25851 original size:81 final size:81
Alignment explanation
Indices: 25765--25978 Score: 250
Period size: 81 Copynumber: 2.6 Consensus size: 81
25755 GTTTCCAGAT
* *** ** * * *
25765 TCGCAACGCAATTTTGACTATCGCGTTGCGATTTTAGAAAATTGCAATGCGAATATGTA-AATCG
1 TCGCAACGCAATTCTGACTATCGCAACGCGATAATACAAAATTGCAACGCGAATATG-ACAATCA
25829 CAACGCGATTCTGACTA
65 CAACGCGATTCTGACTA
* * * *
25846 TCGCAACGTAATTCTGACTATCGCAACGCGATAATACAAAATTGCAACGCGATTCTGACTATCAC
1 TCGCAACGCAATTCTGACTATCGCAACGCGATAATACAAAATTGCAACGCGAATATGACAATCAC
25911 AACGCGATTCTGACTA
66 AACGCGATTCTGACTA
** * * *
25927 TCGCAACGTGATCCTGACTATCACAACGCGATAATAAAAAATTGCAACGCGA
1 TCGCAACGCAATTCTGACTATCGCAACGCGATAATACAAAATTGCAACGCGA
25979 TAGTCCAAGT
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 1 0.01
81 114 0.99
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (81 bp):
TCGCAACGCAATTCTGACTATCGCAACGCGATAATACAAAATTGCAACGCGAATATGACAATCAC
AACGCGATTCTGACTA
Found at i:25979 original size:81 final size:81
Alignment explanation
Indices: 25829--25979 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 81
25819 ATGTAAATCG
* * *
25829 CAACGCGATTCTGACTATCGCAACGTAATTCTGACTATCGCAACGCGATAATACAAAATTGCAAC
1 CAACGCGATTCTGACTATCGCAACGTAATCCTGACTATCACAACGCGATAATAAAAAATTGCAAC
25894 GCGATTCTGACTATCA
66 GCGATTCTGACTATCA
*
25910 CAACGCGATTCTGACTATCGCAACGTGATCCTGACTATCACAACGCGATAATAAAAAATTGCAAC
1 CAACGCGATTCTGACTATCGCAACGTAATCCTGACTATCACAACGCGATAATAAAAAATTGCAAC
25975 GCGAT
66 GCGAT
25980 AGTCCAAGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (81 bp):
CAACGCGATTCTGACTATCGCAACGTAATCCTGACTATCACAACGCGATAATAAAAAATTGCAAC
GCGATTCTGACTATCA
Found at i:25999 original size:21 final size:21
Alignment explanation
Indices: 25975--26021 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
25965 AAATTGCAAC
25975 GCGATAGTCCAAGTTCACGTT
1 GCGATAGTCCAAGTTCACGTT
* *
25996 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCCAAGTTCACGTT
26017 GCGAT
1 GCGAT
26022 TTTCCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (21 bp):
GCGATAGTCCAAGTTCACGTT
Found at i:26129 original size:6 final size:6
Alignment explanation
Indices: 26118--26181 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
26108 GACACGTATT
26118 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
26166 ACC-CG ACC-CG A-CACG A
1 ACCACG ACCACG ACCACG A
26182 GACGAGACGA
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
4 1 0.02
5 11 0.19
6 45 0.79
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:26186 original size:5 final size:5
Alignment explanation
Indices: 26178--26211 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
26168 CCGACCCGAC
* *
26178 ACGAG ACGAG ACGAG ACGAG ACGGG ACGGG ACGA
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
26212 CGGCGGCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.44, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:26516 original size:19 final size:20
Alignment explanation
Indices: 26491--26581 Score: 114
Period size: 19 Copynumber: 4.4 Consensus size: 20
26481 CTTATTTTGG
26491 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
26511 -TTTTTCACTATCGCAACAACAC
1 ATTTTTCACTATCG---CAACAC
26533 ATTTTTCAAACTATCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
*
26555 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
26574 ATTTTTCA
1 ATTTTTCA
26582 AAATCGCGTT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
19 27 0.44
20 5 0.08
21 4 0.06
22 13 0.21
23 6 0.10
25 7 0.11
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:26552 original size:44 final size:41
Alignment explanation
Indices: 26491--26583 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 41
26481 CTTATTTTGG
* *
26491 ATTTTTC--ACTATCGCAACACTTTTTCACTATCGCAACAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCG---CAACAC
26533 ATTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
26574 ATTTTTCAAA
1 ATTTTTCAAA
26584 ATCGCGTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 16 0.34
42 7 0.15
44 24 0.51
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
Found at i:30216 original size:19 final size:19
Alignment explanation
Indices: 30192--30247 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
30182 TCTACATTTT
30192 TATGTGTAGATATTATATA
1 TATGTGTAGATATTATATA
30211 TATGTGTAGATATTATATA
1 TATGTGTAGATATTATATA
*
30230 GATGTGTA-ATATT-TATA
1 TATGTGTAGATATTATATA
30247 T
1 T
30248 TTGAGCATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 26 0.74
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (19 bp):
TATGTGTAGATATTATATA
Found at i:30347 original size:19 final size:19
Alignment explanation
Indices: 30315--30354 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
30305 AATTTTATAA
*
30315 ATTATTTTTTATAAT-TTT
1 ATTATTTTTCATAATATTT
30333 ATTATGTTTTCATAATATTT
1 ATTAT-TTTTCATAATATTT
30353 AT
1 AT
30355 AATATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTATTTTTCATAATATTT
Found at i:30559 original size:29 final size:28
Alignment explanation
Indices: 30508--30588 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 28
30498 GAAAATTTTA
* * *
30508 TAAAACAATATTA-TAATATATAATTAT
1 TAAAAAAATATAATTAATATATAAATAT
30535 TAAAAAAATATAATTAATATTATAAATAT
1 TAAAAAAATATAATTAATA-TATAAATAT
* *
30564 AACAAAAAACTATAATATAAAATAT
1 TA-AAAAAA-TATAAT-TAATATAT
30589 CATAAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 11 0.25
28 5 0.11
29 9 0.20
30 6 0.14
31 9 0.20
32 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAAAAATATAATTAATATATAAATAT
Found at i:34155 original size:29 final size:27
Alignment explanation
Indices: 34108--34178 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
34098 GGCTTGCGTG
*
34108 AAAAAATAATTAGTAATTATATAAATATA
1 AAAAAATAATTA-AAATTATATAAATA-A
*
34137 AAAAAATAATTAAACATTATATTAATAA
1 AAAAAATAATTAAA-ATTATATAAATAA
*
34165 AAAAATTAAATTAA
1 AAAAAAT-AATTAA
34179 CTTGTTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.22
29 29 0.78
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAAAATAATTAAAATTATATAAATAA
Found at i:35102 original size:40 final size:41
Alignment explanation
Indices: 35056--35153 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
35046 AAAAAATAAA
*
35056 ACTCATTTACCCTTATTTTG-AAAAAAAACATGTAACACAT
1 ACTCATTTACCCTTATTTTGAAAAAAAAACATATAACACAT
* *
35096 TCTCATTTTCCCTTATTTTGAAAAAAAAACATATAACACAT
1 ACTCATTTACCCTTATTTTGAAAAAAAAACATATAACACAT
*
35137 ACTCATTTCCCCTTATT
1 ACTCATTTACCCTTATT
35154 GACTTACACC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
40 18 0.35
41 34 0.65
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (41 bp):
ACTCATTTACCCTTATTTTGAAAAAAAAACATATAACACAT
Found at i:36245 original size:9 final size:9
Alignment explanation
Indices: 36231--36273 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
36221 ATCATTAATT
36231 TTATGTTCA
1 TTATGTTCA
36240 TTATGTTCA
1 TTATGTTCA
*
36249 GTCTAGTGTTGA
1 -T-TA-TGTTCA
36261 TTATGTTCA
1 TTATGTTCA
36270 TTAT
1 TTAT
36274 CTCTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 18 0.62
10 3 0.10
11 3 0.10
12 5 0.17
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (9 bp):
TTATGTTCA
Found at i:37069 original size:14 final size:16
Alignment explanation
Indices: 37050--37092 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
37040 TACTAGACAC
37050 ATATATTATCATA-A-
1 ATATATTATCATACAT
37064 ATATATTATC-TACAT
1 ATATATTATCATACAT
37079 ATATATTATTCATA
1 ATATATTA-TCATA
37093 TTTATTCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 8 0.32
16 2 0.08
17 2 0.08
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATTATCATACAT
Found at i:37124 original size:41 final size:40
Alignment explanation
Indices: 37049--37127 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
37039 ATACTAGACA
* * *
37049 CATATATTATCATAAATATATTATCTACATATATATTATT
1 CATATATTATCATAAACATAATATCAACATATATATTATT
37089 CATAT-TTATTCAGTAAACATAATATCAACATATATATTA
1 CATATATTA-TCA-TAAACATAATATCAACATATATATTA
37128 ACCACCTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 3 0.09
40 8 0.24
41 23 0.68
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (40 bp):
CATATATTATCATAAACATAATATCAACATATATATTATT
Found at i:37167 original size:27 final size:27
Alignment explanation
Indices: 37118--37169 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
37108 TAATATCAAC
* *
37118 ATATATATTAACCACCTACAATCAGAA
1 ATATATATTAACAACATACAATCAGAA
* *
37145 ATATATATTCACAACATATAATCAG
1 ATATATATTAACAACATACAATCAG
37170 TAAAGCATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (27 bp):
ATATATATTAACAACATACAATCAGAA
Found at i:38716 original size:15 final size:15
Alignment explanation
Indices: 38696--38725 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38686 ATGAGGGAAT
38696 TGAATTCCATCCAAG
1 TGAATTCCATCCAAG
38711 TGAATTCCATCCAAG
1 TGAATTCCATCCAAG
38726 AATGGATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
TGAATTCCATCCAAG
Found at i:42275 original size:30 final size:30
Alignment explanation
Indices: 42235--42298 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
42225 TGAATTTGTA
* * * *
42235 TTTTGTTATTTTAGTCATTTAATTTTATGT
1 TTTTGCTATTTAACTCATTTAATTTCATGT
*
42265 TTTTGCTATTTAACTCCTTTAATTTCATGT
1 TTTTGCTATTTAACTCATTTAATTTCATGT
42295 TTTT
1 TTTT
42299 AAAATTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.64
Consensus pattern (30 bp):
TTTTGCTATTTAACTCATTTAATTTCATGT
Found at i:45615 original size:15 final size:14
Alignment explanation
Indices: 45588--45628 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
45578 AACAAAGAGC
45588 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
45602 AAAAAGAAATAAAAG
1 AAAAAGAAA-AAAAG
*
45617 AGCAAAGAAAAA
1 A-AAAAGAAAAA
45629 GAAAAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 8 0.33
16 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:45639 original size:17 final size:17
Alignment explanation
Indices: 45604--45646 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
45594 AAAAAAAGAA
* *
45604 AAAGAAATA-AAAGAGC
1 AAAGAAAAAGAAAAAGC
45620 AAAGAAAAAGAAAAAGC
1 AAAGAAAAAGAAAAAGC
45637 AAAGAAAAAG
1 AAAGAAAAAG
45647 GAACAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGC
Found at i:47409 original size:64 final size:64
Alignment explanation
Indices: 47308--47501 Score: 352
Period size: 64 Copynumber: 3.0 Consensus size: 64
47298 AAGCTGTATG
* *
47308 TCAACAAACAACGTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
47372 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
47436 TCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
47500 TC
1 TC
47502 GAAGTGACAC
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 125 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:47719 original size:90 final size:90
Alignment explanation
Indices: 47566--47755 Score: 285
Period size: 90 Copynumber: 2.1 Consensus size: 90
47556 AATTCAAGGC
*
47566 TCAACTTCATAACGAATGGGCCATCCACAATTTCAACTTCACGACGAATGATATCGAGCCCACCA
1 TCAACTTCACAACGAATGGGCCATCCACAATTTCAACTTCACGACGAATGATATCGAGCCCACCA
* *
47631 GCAACATTCATCTTCAGCTTGGATT
66 GCAACATTCATATTCAGATTGGATT
* * *
47656 TCAACTTCACAACGAA-GGGTCCATCCACGATTTCAACTTCACGACGAA-GAATATCGTGTCCAC
1 TCAACTTCACAACGAATGGG-CCATCCACAATTTCAACTTCACGACGAATG-ATATCGAGCCCAC
*
47719 CAGCAACATTCATATTTAGATTGGATT
64 CAGCAACATTCATATTCAGATTGGATT
47746 TCAACTTCAC
1 TCAACTTCAC
47756 GATAAAGGAT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
89 4 0.04
90 87 0.96
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (90 bp):
TCAACTTCACAACGAATGGGCCATCCACAATTTCAACTTCACGACGAATGATATCGAGCCCACCA
GCAACATTCATATTCAGATTGGATT
Found at i:48232 original size:129 final size:129
Alignment explanation
Indices: 47997--48297 Score: 415
Period size: 129 Copynumber: 2.3 Consensus size: 129
47987 AAGATATCCA
* * * **
47997 ACCTGACCTGATCTCCTCATCATGTAGGAACCGCGTTAACCCTAGCTAACCAACCGTCCTCATCA
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGAGTTAACCCTAAATAACCAACCGTCCTCATCA
* * * * *
48062 CATAGTAACAGTGTTATCACCCTTAGATGGCCTGTTGTCCTCATCACGTAAGAATTGTGTCATC
66 CATAGGAACAGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACATAAGAATCGTGTCATC
* *
48126 ACCTAACCTGATCTCCTCATCACGTAGGAGCCGAGTTAA-CCTCAAATAACCAGCCGTCCTCATC
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGAGTTAACCCT-AAATAACCAACCGTCCTCATC
* * * *
48190 ACGTAGGAACCGTGTTATCACCCTTAGATGACTTGTCGTCCTCATCACATAGGAATCGTGTCATC
65 ACATAGGAACAGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACATAAGAATCGTGTCATC
* * *
48255 ACATGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAACCCT
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGAGTTAACCCT
48298 TAGACGACCA
Statistics
Matches: 150, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
128 3 0.02
129 144 0.96
130 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (129 bp):
ACCTGACCTGATCTCCTCATCACGTAGGAGCCGAGTTAACCCTAAATAACCAACCGTCCTCATCA
CATAGGAACAGTGTTATCACCCTTAGATGACCTGTCGTCCTCATCACATAAGAATCGTGTCATC
Found at i:51279 original size:14 final size:14
Alignment explanation
Indices: 51249--51288 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
51239 TTAACAATGC
51249 ATTAATTTATTTAAAT
1 ATTAATTTA--TAAAT
51265 ATTAATTTATAAAT
1 ATTAATTTATAAAT
51279 ATTAATTTAT
1 ATTAATTTAT
51289 TTAGTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
16 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTAATTTATAAAT
Found at i:54430 original size:2 final size:2
Alignment explanation
Indices: 54423--54469 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
54413 ATTTTTAAAA
*
54423 AT AT AT AT -T AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54463 CAT AT AT
1 -AT AT AT
54470 GCATATTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54729 original size:25 final size:25
Alignment explanation
Indices: 54674--54730 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
54664 ATAAATTTCA
*
54674 ATTAATCCAAAATTTGTAAGTCCTG
1 ATTAATCCAAAATTTGCAAGTCCTG
* * *
54699 ACTAATTCAAATTTTGCAAGT-CTCG
1 ATTAATCCAAAATTTGCAAGTCCT-G
54724 ATTAATC
1 ATTAATC
54731 TATTAAGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (25 bp):
ATTAATCCAAAATTTGCAAGTCCTG
Found at i:59321 original size:65 final size:66
Alignment explanation
Indices: 59231--59361 Score: 203
Period size: 65 Copynumber: 2.0 Consensus size: 66
59221 AAATATTGGT
*
59231 CAAAAGGTCATATTGGATTTGTTTTCTAAATTAAAGGGTCACATTGAG-AAAAAATAATATGAGG
1 CAAAAGGTCATATTGGATTTATTTTCTAAATTAAAGGGTCACATTGAGAAAAAAATAATATGAGG
59295 A
66 A
* *
59296 CAAAAGGTCATATTAGG-TTTATTTTCTGAATTAAAGGGTCGCATTGAGAAAAAAAATAATATGA
1 CAAAAGGTCATATT-GGATTTATTTTCTAAATTAAAGGGTCACATTGAG-AAAAAAATAATATGA
59360 GG
64 GG
59362 GTCACATTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
65 42 0.70
66 2 0.03
67 16 0.27
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (66 bp):
CAAAAGGTCATATTGGATTTATTTTCTAAATTAAAGGGTCACATTGAGAAAAAAATAATATGAGG
A
Found at i:59385 original size:28 final size:29
Alignment explanation
Indices: 59330--59388 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 29
59320 TCTGAATTAA
*
59330 AGGGTCGCATTGAGAAAAAAAATAATATG
1 AGGGTCACATTGAGAAAAAAAATAATATG
59359 AGGGTCACATTGAG-AAAAAAATAATATG
1 AGGGTCACATTGAGAAAAAAAATAATATG
59387 AG
1 AG
59389 ACTACATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.20
Consensus pattern (29 bp):
AGGGTCACATTGAGAAAAAAAATAATATG
Found at i:60995 original size:182 final size:181
Alignment explanation
Indices: 60592--61065 Score: 646
Period size: 182 Copynumber: 2.6 Consensus size: 181
60582 GATCCAACTT
* * * * * **
60592 AAAAATGTATCGATCCACAACGATATAACATGTAAAACTATGATAAGACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAAAGATATAACATGTAAAAATATGATAAAACGA-TATCAAAATGATA
* * ** *
60657 AAACCGGTAAAGCGGTACCAAATATATTTAAAA-TGTCGGTACTTTAATATAAGGATCGACACTT
65 AAACCGGTAAAACGATACCGGATATA-TTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
60721 CGTTAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
129 CGTGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * * *
60774 AATAATATATCGATCAACAAAGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGATG
1 AAAAATGTATCGATCAACAAAGATATAACATGTAAAAATATGATAAAAC-GATATCAAAATGATA
* * * * *
60839 AAACCGGTAAAACGTTATCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
60903 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
130 GTGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* *
60955 AAAAATGTATCGATCAGACAATGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATCA-ACAAAGATATAACATGTAAAAATATGATAAAA-CGATATCAAAATGAT
*
61020 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
64 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
61066 CGTAAGTACG
Statistics
Matches: 254, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
181 86 0.34
182 166 0.65
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCAACAAAGATATAACATGTAAAAATATGATAAAACGATATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:61034 original size:17 final size:19
Alignment explanation
Indices: 60995--61037 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
60985 ATGTAAAAAT
60995 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
61015 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
61032 ATGATA
1 ATGATA
61038 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:62842 original size:20 final size:21
Alignment explanation
Indices: 62805--62844 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
62795 AAATTAAGTT
62805 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
62826 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
62845 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:64701 original size:117 final size:117
Alignment explanation
Indices: 64498--64709 Score: 261
Period size: 117 Copynumber: 1.8 Consensus size: 117
64488 ATCTTATTTT
*
64498 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
*
64563 TAAAATCGGAAAACTTTGAAAAAGAAAATTTCAAATTAAACAAACTTCTTCTA
66 TAAAATCGGAAAAC-TTGGAAAAGAAAATTTCAAATTAAACAAACTTCTTCTA
* * * * *
64616 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAAAAAGAAGTTAGAGCTTTCAAA
* ** *
64678 GATAAAATTTG-AAAGTATGGAAAAGAAAATTT
64 AATAAAATCGGAAAACT-TGGAAAAGAAAATTT
64710 TCGATTTAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
115 1 0.01
116 20 0.25
117 55 0.69
118 4 0.05
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (117 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGGAAAACTTGGAAAAGAAAATTTCAAATTAAACAAACTTCTTCTA
Found at i:65283 original size:20 final size:21
Alignment explanation
Indices: 65250--65289 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
65240 TTTTAACATA
65250 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
65270 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
65290 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:65297 original size:22 final size:20
Alignment explanation
Indices: 65239--65293 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
65229 CTTGGTCAAA
*
65239 ATTTTAACATAATTGATATTC
1 ATTTTAA-ACAATTGATATTC
*
65260 ATTTTAAACCATTGATA-TC
1 ATTTTAAACAATTGATATTC
65279 AATTTTCAAACAATT
1 -ATTTT-AAACAATT
65294 TGATTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.45
21 14 0.48
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTTAAACAATTGATATTC
Found at i:68671 original size:44 final size:44
Alignment explanation
Indices: 68621--68716 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
68611 CTTCATGCAC
* * * *
68621 CGATGCATTTAACA-ATGCATCGATGCATCCCTTTGAATATGTAT
1 CGATGCATTCAACAGATGCACCGATGCATCCC-TTGAATAGGCAT
* *
68665 CGATGCA-TCACCATGATGCACCGATGCATGCCTTGAATAGGCAT
1 CGATGCATTCAACA-GATGCACCGATGCATCCCTTGAATAGGCAT
68709 CGATGCAT
1 CGATGCAT
68717 AAGACCATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 4 0.09
44 24 0.56
45 15 0.35
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
CGATGCATTCAACAGATGCACCGATGCATCCCTTGAATAGGCAT
Found at i:69997 original size:20 final size:21
Alignment explanation
Indices: 69960--69999 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
69950 AAATTAAGTT
69960 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
69981 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
70000 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:71495 original size:182 final size:182
Alignment explanation
Indices: 70975--71876 Score: 1553
Period size: 182 Copynumber: 5.0 Consensus size: 182
70965 TAACTCAACA
* *
70975 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGATACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* * * *
71040 AAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTGGATAGTTTATAAAAATATATCGATCTATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
71104 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
71156 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* *
71218 AATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGTTACTTTATAAAAATGTATCGATCCATAA
66 AA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* * * *
71283 CAATATAACATGTAAAAATATGACAAAACCGGTTTGGAAATGACAACATAGGT
130 CAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
71336 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
71401 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
*
71466 AATATAACATGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
71518 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
*
71583 AAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
71648 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
* *
71700 AAAGCGCTACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA-TT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* *
71764 AATAAGAGAAGAAGTTATAGTGCCAATAAAGTATCGATACTTTATAAAAATGTATCGATCCATAA
66 AA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* * **
71829 TAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
130 CAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
71877 GGTGAACGCA
Statistics
Matches: 688, Mismatches: 27, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
178 4 0.01
179 18 0.03
180 146 0.21
181 53 0.08
182 463 0.67
183 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (182 bp):
AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
Found at i:72110 original size:87 final size:87
Alignment explanation
Indices: 72012--72174 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
72002 AATTTGGTCA
*
72012 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
72077 CCGGTTAAATACTTATTTTATT
66 CCGGTTAAATACTTATTTTATT
* *
72099 ATATAAGCGCTATCTATTACATTATATAAACGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
*
72164 CTGGTTAAATA
66 CCGGTTAAATA
72175 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACTTATTTTATT
Found at i:73580 original size:37 final size:37
Alignment explanation
Indices: 73525--73636 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
73515 AACATAACGT
* *
73525 TAGAGTTTTATTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
73562 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
73599 TAGAGTTTTACTATAATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
73636 T
1 T
73637 CCATAAGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:76313 original size:103 final size:103
Alignment explanation
Indices: 76122--76323 Score: 296
Period size: 103 Copynumber: 2.0 Consensus size: 103
76112 AGAACATATT
* * * *
76122 AGCACACACAGTGCTATCATATCAGAATCATAATATGGACACAAAGTGCAATCACATCTGAAATA
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATATGAAATA
* * * *
76187 TACTAGTGTACCTACGGGCAACACCACAGTATATCATA
66 TACTAGTGTACCCACCGACAACACCACAATATATCATA
* *
76225 AGCACACACAATGCTATCACATCAGATTCATAATATGCACACAAAGTGCAATCATATATGAAATA
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATATGAAATA
* *
76290 TACTAGTGTACCCACCGATAACACGACAATATAT
66 TACTAGTGTACCCACCGACAACACCACAATATAT
76324 TAATCACTCC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (103 bp):
AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATATGAAATA
TACTAGTGTACCCACCGACAACACCACAATATATCATA
Found at i:79278 original size:29 final size:29
Alignment explanation
Indices: 79198--79279 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
79188 AAAATATATT
*
79198 ACTTTTCAAAATTACATTTTTA-TCCCTAA
1 ACTTTTCAAAATTACA-TTTTAGCCCCTAA
* *
79227 ACTTTTACAAAATTTATACTTTAGCCCCTAA
1 ACTTTT-CAAAA-TTACATTTTAGCCCCTAA
79258 A-TTTTCAAAACTTACATTTTAG
1 ACTTTTCAAAA-TTACATTTTAG
79280 TCACTAGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 20 0.45
30 13 0.30
31 11 0.25
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (29 bp):
ACTTTTCAAAATTACATTTTAGCCCCTAA
Found at i:83926 original size:16 final size:18
Alignment explanation
Indices: 83905--83937 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
83895 ATGCTACGAC
83905 ATTCATC-AAAA-AAACA
1 ATTCATCTAAAATAAACA
83921 ATTCATCTAAAATAAAC
1 ATTCATCTAAAATAAAC
83938 CCAAGCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTCATCTAAAATAAACA
Found at i:86791 original size:37 final size:37
Alignment explanation
Indices: 86741--86848 Score: 130
Period size: 37 Copynumber: 2.9 Consensus size: 37
86731 TTTAAATTTA
* *
86741 ATTAAATTTGAATA-GTTATTTATGAATTTATATTCG
1 ATTAAATATGAATATATTATTTATGAATTTATATTCG
* *
86777 ATTGAAATATGAATATATTATTTAT-AAATTATATTTG
1 ATT-AAATATGAATATATTATTTATGAATTTATATTCG
***
86814 ATTAAATGCAAATATATTATTTATGAATTTATATT
1 ATTAAATATGAATATATTATTTATGAATTTATATT
86849 ATATATAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 21 0.34
37 32 0.52
38 8 0.13
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (37 bp):
ATTAAATATGAATATATTATTTATGAATTTATATTCG
Done.